Starting phenix.real_space_refine on Wed Jan 15 20:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270.map" model { file = "/net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9faa_50270/01_2025/9faa_50270_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2815 2.51 5 N 730 2.21 5 O 905 1.98 5 H 4235 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8695 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1725 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.85, per 1000 atoms: 0.44 Number of scatterers: 8695 At special positions: 0 Unit cell: (88.011, 124.46, 42.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 905 8.00 N 730 7.00 C 2815 6.00 H 4235 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 783.0 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.194A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.360A pdb=" N VAL D 10 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.672A pdb=" N THR A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS B 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 21 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.588A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.779A pdb=" N GLN D 36 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN A 36 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 36 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52 removed outlier: 6.662A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 65 removed outlier: 6.621A pdb=" N SER A 62 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASN B 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.788A pdb=" N LEU D 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER B 75 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 74 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER C 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 74 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER E 75 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 74 " --> pdb=" O SER E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 86 removed outlier: 6.542A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 97 removed outlier: 6.457A pdb=" N TRP D 90 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR B 93 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 92 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 95 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE B 97 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 96 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 97 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR C 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 92 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE C 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 96 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR E 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 92 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL E 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE E 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 96 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106 removed outlier: 6.707A pdb=" N LEU D 103 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU B 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 105 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 103 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 105 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU C 103 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 105 " --> pdb=" O LEU E 106 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4235 1.03 - 1.22: 5 1.22 - 1.42: 1960 1.42 - 1.61: 2600 1.61 - 1.81: 10 Bond restraints: 8810 Sorted by residual: bond pdb=" CB ILE E 20 " pdb=" CG2 ILE E 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" CB ILE B 20 " pdb=" CG2 ILE B 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 1.516 1.498 0.018 1.18e-02 7.18e+03 2.34e+00 bond pdb=" CB ILE C 20 " pdb=" CG2 ILE C 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB ILE A 20 " pdb=" CG2 ILE A 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.29e+00 ... (remaining 8805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14447 1.41 - 2.82: 1160 2.82 - 4.23: 173 4.23 - 5.64: 40 5.64 - 7.05: 10 Bond angle restraints: 15830 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.94 102.89 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 109.94 102.91 7.03 1.57e+00 4.06e-01 2.00e+01 angle pdb=" N THR E 69 " pdb=" CA THR E 69 " pdb=" C THR E 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR B 69 " pdb=" CA THR B 69 " pdb=" C THR B 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR C 69 " pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 109.94 102.95 6.99 1.57e+00 4.06e-01 1.98e+01 ... (remaining 15825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3764 14.86 - 29.73: 338 29.73 - 44.59: 111 44.59 - 59.45: 95 59.45 - 74.31: 30 Dihedral angle restraints: 4338 sinusoidal: 2378 harmonic: 1960 Sorted by residual: dihedral pdb=" CA PHE B 61 " pdb=" C PHE B 61 " pdb=" N SER B 62 " pdb=" CA SER B 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" CA PHE D 61 " pdb=" C PHE D 61 " pdb=" N SER D 62 " pdb=" CA SER D 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA PHE E 61 " pdb=" C PHE E 61 " pdb=" N SER E 62 " pdb=" CA SER E 62 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 476 0.048 - 0.096: 181 0.096 - 0.144: 43 0.144 - 0.192: 0 0.192 - 0.241: 5 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG E 201 " pdb=" ND2 ASN E 19 " pdb=" C2 NAG E 201 " pdb=" O5 NAG E 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 702 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 49 " 0.029 2.00e-02 2.50e+03 3.69e-02 2.04e+01 pdb=" CD GLN E 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN E 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN E 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN E 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN E 49 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN D 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN D 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN D 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN D 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN D 49 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN A 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN A 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 49 " 0.056 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 187 2.09 - 2.72: 14912 2.72 - 3.34: 22425 3.34 - 3.97: 31298 3.97 - 4.60: 46361 Nonbonded interactions: 115183 Sorted by model distance: nonbonded pdb=" H ASN A 68 " pdb=" OD1 ASN B 68 " model vdw 1.461 2.450 nonbonded pdb=" OD1 ASN A 68 " pdb=" H ASN C 68 " model vdw 1.553 2.450 nonbonded pdb=" OD1 ASN C 68 " pdb=" H ASN E 68 " model vdw 1.598 2.450 nonbonded pdb=" OD1 ASN D 68 " pdb=" H ASN B 68 " model vdw 1.649 2.450 nonbonded pdb="HG21 THR E 69 " pdb=" H ALA E 70 " model vdw 1.788 2.270 ... (remaining 115178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.053 4575 Z= 0.675 Angle : 1.099 7.048 6240 Z= 0.623 Chirality : 0.053 0.241 705 Planarity : 0.006 0.042 805 Dihedral : 11.734 74.313 1690 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 90 PHE 0.021 0.005 PHE C 61 TYR 0.038 0.007 TYR B 85 ARG 0.009 0.003 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8275 (t) cc_final: 0.7998 (m) REVERT: A 91 ASP cc_start: 0.7857 (t0) cc_final: 0.7645 (t0) REVERT: A 108 GLN cc_start: 0.7845 (pt0) cc_final: 0.7535 (pp30) REVERT: A 117 LEU cc_start: 0.5983 (mt) cc_final: 0.5694 (mt) REVERT: D 49 GLN cc_start: 0.7584 (tt0) cc_final: 0.7383 (tt0) REVERT: D 108 GLN cc_start: 0.7793 (pt0) cc_final: 0.7496 (pp30) REVERT: C 108 GLN cc_start: 0.7868 (pt0) cc_final: 0.7408 (pp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2760 time to fit residues: 27.6890 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.123027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.104423 restraints weight = 26249.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.108016 restraints weight = 10047.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.110310 restraints weight = 5290.453| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4575 Z= 0.184 Angle : 0.616 4.358 6240 Z= 0.324 Chirality : 0.051 0.252 705 Planarity : 0.005 0.045 805 Dihedral : 6.183 23.544 730 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.22 % Allowed : 4.69 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 PHE 0.013 0.001 PHE D 2 TYR 0.014 0.002 TYR C 85 ARG 0.003 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8280 (t) cc_final: 0.7918 (m) REVERT: A 108 GLN cc_start: 0.7819 (pt0) cc_final: 0.7449 (pp30) REVERT: A 117 LEU cc_start: 0.6401 (mt) cc_final: 0.6196 (mt) REVERT: D 108 GLN cc_start: 0.7808 (pt0) cc_final: 0.7365 (pp30) REVERT: C 91 ASP cc_start: 0.7769 (t0) cc_final: 0.7303 (m-30) REVERT: C 108 GLN cc_start: 0.7913 (pt0) cc_final: 0.7297 (pp30) REVERT: E 91 ASP cc_start: 0.8000 (t0) cc_final: 0.7367 (m-30) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.2760 time to fit residues: 23.7310 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain B residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.118498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.100810 restraints weight = 28071.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.104347 restraints weight = 10819.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.106545 restraints weight = 5597.351| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4575 Z= 0.322 Angle : 0.665 6.125 6240 Z= 0.347 Chirality : 0.049 0.203 705 Planarity : 0.005 0.042 805 Dihedral : 6.632 32.549 730 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.63 % Allowed : 5.92 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 PHE 0.013 0.002 PHE B 61 TYR 0.019 0.002 TYR D 85 ARG 0.001 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8279 (t) cc_final: 0.7910 (m) REVERT: A 91 ASP cc_start: 0.7721 (t0) cc_final: 0.7501 (t0) REVERT: A 108 GLN cc_start: 0.7912 (pt0) cc_final: 0.7461 (pp30) REVERT: D 108 GLN cc_start: 0.7938 (pt0) cc_final: 0.7495 (pp30) REVERT: C 108 GLN cc_start: 0.8012 (pt0) cc_final: 0.7168 (pp30) REVERT: E 91 ASP cc_start: 0.8049 (t0) cc_final: 0.7319 (m-30) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.2915 time to fit residues: 23.4300 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.116380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.099095 restraints weight = 28417.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.102426 restraints weight = 11063.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104525 restraints weight = 5813.014| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4575 Z= 0.345 Angle : 0.664 5.857 6240 Z= 0.350 Chirality : 0.048 0.214 705 Planarity : 0.006 0.040 805 Dihedral : 6.929 35.664 730 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.04 % Allowed : 7.55 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 34 PHE 0.015 0.002 PHE A 61 TYR 0.017 0.002 TYR A 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8394 (t) cc_final: 0.8032 (m) REVERT: A 108 GLN cc_start: 0.7878 (pt0) cc_final: 0.6949 (pp30) REVERT: D 108 GLN cc_start: 0.8080 (pt0) cc_final: 0.7533 (pp30) REVERT: C 108 GLN cc_start: 0.8068 (pt0) cc_final: 0.7261 (pp30) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.2807 time to fit residues: 24.0251 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.119302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.101941 restraints weight = 27568.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.105438 restraints weight = 10570.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.107668 restraints weight = 5473.519| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4575 Z= 0.183 Angle : 0.568 4.212 6240 Z= 0.295 Chirality : 0.049 0.224 705 Planarity : 0.005 0.044 805 Dihedral : 6.310 31.057 730 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.63 % Allowed : 8.98 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 34 PHE 0.010 0.001 PHE B 61 TYR 0.010 0.001 TYR A 85 ARG 0.002 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8334 (t) cc_final: 0.7927 (m) REVERT: A 108 GLN cc_start: 0.7885 (pt0) cc_final: 0.6942 (pp30) REVERT: D 108 GLN cc_start: 0.8065 (pt0) cc_final: 0.7524 (pp30) REVERT: C 108 GLN cc_start: 0.8014 (pt0) cc_final: 0.7224 (pp30) REVERT: E 91 ASP cc_start: 0.7997 (t0) cc_final: 0.7335 (m-30) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.2799 time to fit residues: 23.3007 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.118248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.101184 restraints weight = 27882.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.104489 restraints weight = 10936.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.106598 restraints weight = 5801.088| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4575 Z= 0.261 Angle : 0.594 4.484 6240 Z= 0.310 Chirality : 0.047 0.204 705 Planarity : 0.005 0.046 805 Dihedral : 6.569 34.834 730 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.04 % Allowed : 9.39 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.012 0.001 PHE A 61 TYR 0.013 0.002 TYR C 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8374 (t) cc_final: 0.7965 (m) REVERT: D 108 GLN cc_start: 0.8078 (pt0) cc_final: 0.7526 (pp30) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.2871 time to fit residues: 23.5765 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.120037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.102612 restraints weight = 27626.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.106124 restraints weight = 10481.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.108249 restraints weight = 5442.592| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4575 Z= 0.156 Angle : 0.545 4.119 6240 Z= 0.284 Chirality : 0.048 0.218 705 Planarity : 0.005 0.047 805 Dihedral : 6.020 29.256 730 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.02 % Allowed : 10.20 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 90 PHE 0.010 0.001 PHE D 61 TYR 0.007 0.001 TYR E 26 ARG 0.001 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8398 (t) cc_final: 0.7951 (m) REVERT: D 108 GLN cc_start: 0.8068 (pt0) cc_final: 0.7505 (pp30) outliers start: 5 outliers final: 5 residues processed: 58 average time/residue: 0.2880 time to fit residues: 22.3142 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 overall best weight: 0.5148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.122080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.104899 restraints weight = 27671.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.108351 restraints weight = 10662.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.110582 restraints weight = 5562.467| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4575 Z= 0.141 Angle : 0.528 4.056 6240 Z= 0.271 Chirality : 0.047 0.201 705 Planarity : 0.005 0.045 805 Dihedral : 5.664 25.782 730 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.43 % Allowed : 11.22 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 90 PHE 0.010 0.001 PHE D 61 TYR 0.006 0.001 TYR C 85 ARG 0.002 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 GLN cc_start: 0.8108 (pt0) cc_final: 0.7454 (pp30) REVERT: B 108 GLN cc_start: 0.7436 (pt0) cc_final: 0.7090 (pp30) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.2888 time to fit residues: 21.8408 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.118326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.101192 restraints weight = 28050.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.104513 restraints weight = 10789.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.106539 restraints weight = 5666.962| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4575 Z= 0.298 Angle : 0.604 5.002 6240 Z= 0.314 Chirality : 0.047 0.190 705 Planarity : 0.005 0.045 805 Dihedral : 6.438 35.996 730 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.22 % Allowed : 11.43 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 34 PHE 0.012 0.002 PHE A 61 TYR 0.014 0.002 TYR E 85 ARG 0.001 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8403 (t) cc_final: 0.7947 (m) REVERT: D 108 GLN cc_start: 0.8152 (pt0) cc_final: 0.7551 (pp30) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.2822 time to fit residues: 20.5215 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.121110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.103820 restraints weight = 27789.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.107368 restraints weight = 10502.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.109569 restraints weight = 5407.071| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4575 Z= 0.151 Angle : 0.529 3.866 6240 Z= 0.273 Chirality : 0.048 0.208 705 Planarity : 0.005 0.046 805 Dihedral : 5.827 29.351 730 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.02 % Allowed : 11.84 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 90 PHE 0.010 0.001 PHE D 61 TYR 0.006 0.001 TYR C 85 ARG 0.001 0.000 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 GLN cc_start: 0.8097 (pt0) cc_final: 0.7496 (pp30) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.2828 time to fit residues: 20.9882 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.103904 restraints weight = 27639.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.107302 restraints weight = 10621.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.109439 restraints weight = 5543.386| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4575 Z= 0.167 Angle : 0.531 4.012 6240 Z= 0.272 Chirality : 0.047 0.193 705 Planarity : 0.005 0.045 805 Dihedral : 5.783 29.319 730 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.22 % Allowed : 11.63 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 34 PHE 0.010 0.001 PHE D 61 TYR 0.007 0.001 TYR C 85 ARG 0.001 0.000 ARG C 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.69 seconds wall clock time: 59 minutes 41.07 seconds (3581.07 seconds total)